#MD01_2412.Harada.2006
---
title: "MD01_2412.Harada.2006"
output:
flexdashboard::flex_dashboard:
vertical_layout: scroll
theme: bootstrap
source_code: embed
orientation: rows
---
```{r setup, include = FALSE}
library(flexdashboard)
library(maptools)
library(tidyverse)
library(purrr)
library(leaflet)
library(plotly)
library(lipdR)
library(dygraphs)
library(geoChronR)
library(lipdverseR)
#read functions
load("../../temp.Rdata")
load("../../chronTemp.Rdata")
#remove columns we don't want to plot
varNames <- sapply(TS, "[[","paleoData_variableName")
# good <- which(!(varNames %in% c("year","depth","age")))
# TS <- TS[good]
#All datasets
dsn <- lipdR::pullTsVariable(TS,"dataSetName")
ui <- which(!duplicated(dsn))
udsn <- dsn[ui]
lat <- lipdR::pullTsVariable(TS,"geo_latitude")[ui]
lon <- lipdR::pullTsVariable(TS,"geo_longitude")[ui]
elev <- lipdR::pullTsVariable(TS,"geo_elevation")[ui]
archiveType <- lipdR::pullTsVariable(TS,"archiveType")[ui]
link <- paste0(udsn,".html") %>%
str_replace_all("'","_")
#Organize metadata for map
map.meta <- data.frame(dataSetName = udsn, #datasetname
lat = lat,#lat
lon = lon,#lon
# elev = elev,#elevation
archiveType = factor(archiveType),#archiveType
link = link)#Link
#set index number
i = 385
thisTS <- TS[which(udsn[i] == dsn)]
```
#MD01_2412.Harada.2006
Metadata {.sidebar}
-------------------------------------
[Download LiPD file](MD01_2412.Harada.2006.lpd)
[Edit LiPD file](http://lipd.net/playground?source=http://lipdverse.org/Temp12k/1_0_2/MD01_2412.Harada.2006.lpd)
[Download paleoData only (csv)](MD01_2412.Harada.2006.csv)
[Download chronData only (csv)](MD01_2412.Harada.2006-chron.csv)
[Report an issue (include dataset name)](https://github.com/nickmckay/LiPDverse/issues)
root
archiveType: MarineSediment
originalDataUrl: www.ncdc.noaa.gov/paleo/study/9096
lipdVersion: 1.3
pub
pub1
author: list(list(name = "Harada, Naomi; Ahagon, Naokazu; Sakamoto, Tatsuhiko; Uchida, Masao; Ikehara, Minoru; Shibata, Yasuyuki"))
citeKey: KUFYKK47
journal: Global and Planetary Change
volume: 53
pages: 29 46
title: Rapid fluctuation of alkenone temperature in the southwestern Okhotsk Sea during the past 120 ky
pub2
geo
latitude: 44.5275
longitude: 145.004
elevation: -1225
siteName: MD01_2412
PaleoData columns
depth (cm)
TSid: T2L_MD01_2412_depth
variableName: depth
units: cm
description: Sample depth
ageDuplicate (cal years BP)
TSid: T2L_MD01_2412_age_median
variableName: ageDuplicate
units: cal years BP
description: Median age
ageOriginal (BP)
TSid: T2L_MD01_2412_age_original
variableName: ageOriginal
units: BP
description: Original age
ageMedianBacon (cal years BP)
TSid: T2L_MD01_2412_age_medianMedianBacon
variableName: ageMedianBacon
units: cal years BP
description: Median age
age (BP)
TSid: T2L_MD01_2412_age
variableName: age
units: BP
description: Original age
temperature (degC)
TSid: T2L_MD01_2412_uk37_SST_from_uk37
variableName: temperature
units: degC
description: SST calculated from uk37
interpretation
1
direction: positive
variable: T
scope: climate
variableGroup: Temperature
variableGroupOriginal: T
seasonality: annual
seasonalityGeneral: annual
seasonalityOriginal: 1 2 3 4 5 6 7 8 9 10 11 12
variableDetail: sea@surface
variableGroupDirection: list("negative")
Uk37 (unitless)
TSid: T2L_MD01_2412_uk37
variableName: Uk37
units: unitless
ChronData columns
depth_top (cm)
TSid: T2L_MD01_2412_depth_top
variableName: depth_top
units: cm
description: Sample top depth
depth_bottom (cm)
TSid: T2L_MD01_2412_depth_bottom
variableName: depth_bottom
units: cm
description: Sample bottom depth
age_type (unitless)
TSid: RC3BPGwHVg7
variableName: age_type
units: unitless
age (yr BP)
TSid: RbW0YiuMOmH
variableName: age
units: yr BP
labcode ()
TSid: T2L_MD01_2412_labcode
variableName: labcode
description: Lab sample code
mat_dated ()
TSid: T2L_MD01_2412_mat_dated
variableName: mat_dated
description: Material dated
c14_date (RC yr BP)
TSid: T2L_MD01_2412_c14_date
variableName: c14_date
units: RC yr BP
description: 14C date
c14_1s_err (RC yr BP)
TSid: T2L_MD01_2412_c14_1s_err
variableName: c14_1s_err
units: RC yr BP
description: 14C 1-sigma error
delta_r ()
TSid: T2L_MD01_2412_delta_r
variableName: delta_r
description: delta R
delta_r_original ()
TSid: T2L_MD01_2412_delta_r_original
variableName: delta_r_original
description: Original delta R
delta_r_1s_error ()
TSid: T2L_MD01_2412_delta_r_1s_error
variableName: delta_r_1s_error
description: delta R 1-sigma error
delta_r_1s_error_original ()
TSid: T2L_MD01_2412_delta_r_1s_error_original
variableName: delta_r_1s_error_original
description: Original delta R 1-sigma error
other_date ()
TSid: T2L_MD01_2412_other_date
variableName: other_date
description: Other date
other_1s_err ()
TSid: T2L_MD01_2412_other_1s_err
variableName: other_1s_err
description: Other date 1-sigma error
other_type ()
TSid: T2L_MD01_2412_other_type
variableName: other_type
description: Other date type
Row {.tabset .tabset-fade}
-----------------------------------------------------------------------
### Sitemap
```{r}
map.meta.split <- split(map.meta, map.meta$archiveType)
factpal <- colorFactor("Paired",map.meta$archiveType)
buff <- 15
l <- leaflet() %>%
addTiles() %>%
fitBounds(map.meta$lon[i]-buff,map.meta$lat[i]-buff,map.meta$lon[i]+buff,map.meta$lat[i]+buff)
names(map.meta.split) %>%
purrr::walk( function(df) {
l <<- l %>%
addMarkers(data=map.meta.split[[df]],
lng=~lon, lat=~lat,
label=~as.character(archiveType),
popup=~paste(str_c('Dataset: ',dataSetName,''),
# str_c("Elevation: ",elev),
str_c("Archive Type: ",archiveType),
sep = "
"),
group = df,
clusterOptions = markerClusterOptions(removeOutsideVisibleBounds = F),
labelOptions = labelOptions(noHide = F,
direction = 'auto'))
})
l <- l %>% addCircleMarkers(lng = map.meta$lon[i], lat = map.meta$lat[i],radius = 20,color = "red",fillColor = "none")
l %>%
addLayersControl(position = "bottomleft",
overlayGroups = names(map.meta.split),
options = layersControlOptions(collapsed = FALSE,
opacity = 0.8)
)
```
### Search the LiPDverse (Beta! doesn't work well yet)
```{r}
#Add google search bar
htmltools::includeHTML("../../googleSearchChunk.html")
```
Row {.tabset .tabset-fade}
-----------------------------------------------------------------------
### temperature (degC)
```{r}
plotCol(thisTS,ind = 5)
```
### Uk37 (unitless)
```{r}
plotCol(thisTS,ind = 4)
```
Row {.tabset .tabset-fade}
-----------------------------------------------------------------------
### depth_top (cm)
```{r}
plotCol(chronTS,ind = 2)
```
### depth_bottom (cm)
```{r}
plotCol(chronTS,ind = 3)
```
### age_type (unitless)
```{r}
plotCol(chronTS,ind = 14)
```
### age (yr BP)
```{r}
plotCol(chronTS,ind = 15)
```
### labcode ()
```{r}
plotCol(chronTS,ind = 1)
```
### mat_dated ()
```{r}
plotCol(chronTS,ind = 4)
```
### c14_date (RC yr BP)
```{r}
plotCol(chronTS,ind = 5)
```
### c14_1s_err (RC yr BP)
```{r}
plotCol(chronTS,ind = 6)
```
### delta_r ()
```{r}
plotCol(chronTS,ind = 7)
```
### delta_r_original ()
```{r}
plotCol(chronTS,ind = 8)
```
### delta_r_1s_error ()
```{r}
plotCol(chronTS,ind = 9)
```
### delta_r_1s_error_original ()
```{r}
plotCol(chronTS,ind = 10)
```
### other_date ()
```{r}
plotCol(chronTS,ind = 11)
```
### other_1s_err ()
```{r}
plotCol(chronTS,ind = 12)
```
### other_type ()
```{r}
plotCol(chronTS,ind = 13)
```